Somatic
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How to recover a mutation from secondary alignment0 votes 0 comments
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Is it ok to use -L for each chromosome separately when running Mutect2?0 votes 0 comments
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Asking for advice on Mutect2 calling in somatic but amplicon data0 votes 0 comments
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How to call somatic variants without normal matched sample (cfDNA)0 votes 0 comments
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Somatic mutations detection using mutect20 votes 0 comments
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GatherPileupSummaries does not sort input variants0 votes 0 comments
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Problem generating germline resource file for Mutect20 votes 0 comments
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GatherVCFs error - provider not installed0 votes 1 comment
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Mutect2 VCF sample order in tumor normal paired call0 votes 0 comments
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How do if remove Germline Variants from my variant calling file ?0 votes 0 comments
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Error - Mutect2 PG tag0 votes 0 comments
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GenomicsDBImport error: USER ERROR has occurred: Duplicate sample: 1. Sample was found in both file: Completed0 votes 12 comments
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sample size for somatic CNV0 votes 1 comment
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Could not find vcf.stats file after Mutect20 votes 2 comments
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Panel of Normals creation error: GenomicsDBImport does not support GVCFs with MNPs Answered0 votes 1 comment
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Can Mutect2 calls tumor sample specific SNV under joint calling mode?0 votes 3 comments
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af-only-gnomad.vcf.gz0 votes 1 comment
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Panel of Normals - inconsistent filtering behavior0 votes 4 comments
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Error while running ModelSegments Answered0 votes 15 comments
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Create Panel of Normals Issue0 votes 2 comments
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Funcotator error: Only IGRs were produced for this dataset Answered0 votes 4 comments
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Mutect2 cannot generate stats file and f1r2.tar.gz file Answered0 votes 4 comments
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GATK Muteck2 missing call Answered1 vote 2 comments
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Picard error (AddOrReplaceReadGroups) Answered0 votes 4 comments
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Issue when running BaseRecalibrator0 votes 5 comments
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Increased number of false positives in Mutect2 GATK 4.1.7.00 votes 15 comments
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improt gcnvkernel fails. somehting to do with theano lock Answered0 votes 3 comments
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Difference between variants detected using gatk 4.1.8.1 and 4.1.9.0 Answered0 votes 2 comments
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Mutect2 filter : clustered_events definition Answered0 votes 7 comments